Kai He

Interglacial refugia preserved high genetic diversity of the Chinese mole shrew in the mountains of southwest China.

The mountains of southwest China (MSC) harbor extremely high species diversity; however, the mechanism behind this diversity is unknown. We investigated to what degree the topography and climate change shaped the genetic diversity and diversification in these mountains, and we also sought to identify the locations of microrefugia areas in these mountains. For these purposes, we sampled extensively to estimate the intraspecific phylogenetic pattern of the Chinese mole shrew (Anourosorex squamipes) in southwest China throughout its range of distribution. Two mitochondrial genes, namely, cytochrome b (CYT B) and NADH dehydrogenase subunit 2 (ND2), from 383 archived specimens from 43 localities were determined for phylogeographic and demographic analyses. We used the continuous-diffusion phylogeographic model, extensive Bayesian skyline plot species distribution modeling (SDM) and approximate Bayesian computation (ABC) to explore the changes in population size and distribution through time of the species. Two phylogenetic clades were identified, and significantly higher genetic diversity was preserved in the southern subregion of the mountains. The results of the SDM, continuous-diffusion phylogeographic model, extensive Bayesian skyline plot and ABC analyses were congruent and supported that the Last Interglacial Maximum (LIG) was an unfavorable period for the mole shrews because of a high degree of seasonality; A. squamipes survived in isolated interglacial refugia mainly located in the southern subregion during the LIG and rapidly expanded during the last glacial period. These results furnished the first evidence for major Pleistocene interglacial refugia and a latitudinal effect in southwest China, and the results shedding light on the higher level of species richness in the southern subregion.

Molecular phylogenetics and phylogeographic structure of Sorex bedfordiae based on mitochondrial and nuclear DNA sequences

The southeastern margin of the Tibetan Plateau is characterized by complex topography and a discontinuous landscape, creating a sky island situation. However, the way topography shapes genetic structures and demographic histories of endemic species has not been well studied. We examined the phylogeographic pattern and demographic histories of Sorex bedfordiae, a dispersal-limited small mammal, using three nuclear genes [1977bp] and two mitochondrial genes [1794bp] with comprehensive molecular approaches. We recovered five well-supported clades whose distributions are along mountain ridges and roughly subdivided by large rivers. Demographic expansions in the middle Pleistocene were strongly supported by both nuclear and mitochondrial genes. Our results support the hypothesis that sky island topography and river systems strongly affect the genetic structure of non-aquatic terrestrial species. We further clarify that S. bedfordiae and S. cylindricauda are valid sibling species, whereas S. excelsus is most likely a geographic subspecies of S. bedfordiae.

A comprehensive phylogeny of the genus Kurixalus (Rhacophoridae, Anura) sheds light on the geographical range evolution of frilled swamp treefrogs

Currently, the genus Kurixalus comprises 14 species distributed in Southern, Southeast and East Asia. Because of their relatively low dispersal capability and intolerance of seawater, this group is ideal for the study of terrestrial range evolution, especially that portion of its range that extends into the island archipelagos of Southern Asia. We assembled a large dataset of mitochondrial and nuclear genes, and estimated phylogeny by maximum likelihood and Bayesian methods, and we explored the history of each species via divergence-time estimation based on fossil-calibrations. A variety of ancestral-area reconstruction strategies were employed to estimate past changes of the species geographical range, and to evaluate the impact of different abiotic barriers on range evolution. We found that frilled swamp treefrogs probably originated in Taiwan or South Vietnam in the Oligocene. Alternatively, the lineage leading to Kurixalus appendiculatus strongly supports a hypothesis of terrestrial connection between the Indian and Asian continents in the Oligocene. The outcome of both our divergence-time estimates and ancestral-area reconstruction suggests that the divergence between species from Indochina and Taiwan can probably be attributed to the opening of the South China Sea, approximately 33u202fmillion years ago. We could not find evidence for dispersal between mainland China and Taiwan Island. Formation of both Mekong and Red River valleys did not have any impact on Kurixalus species diversification. However, coincidence in timing of climate change and availability of plausible dispersal routes from the Oligocene to the middle Miocene, plausibly implied that Kurixalus diversification in Asia resulted from contemporaneous, climate-induced environmental upheaval (Late Oligocene Warming at 29u202fMa; Mi-1 glaciation since 24.4-21.5u202fMa; Mid-Miocene Climatic Optimum at 14u202fMa), which alternatively opened and closed dispersal routes.

Mitochondrial DNA analyses and ecological niche modeling reveal post‐LGM expansion of the Assam macaque (Macaca assamensis) in the foothills of Nepal Himalaya

Genetic diversity of a species is influenced by multiple factors, including the Quaternary glacial‐interglacial cycles and geophysical barriers. Such factors are not yet well documented for fauna from the southern border of the Himalayan region. This study used mitochondrial DNA (mtDNA) sequences and ecological niche modeling (ENM) to explore how the late Pleistocene climatic fluctuations and complex geography of the Himalayan region have shaped genetic diversity, population genetic structure, and demographic history of the Nepalese population of Assam macaques (Macaca assamensis) in the Himalayan foothills. A total of 277 fecal samples were collected from 39 wild troops over almost the entire distribution of the species in Nepal. The mtDNA fragment encompassing the complete control region (1121u2009bp) was recovered from 208 samples, thus defining 54 haplotypes. Results showed low nucleotide diversity (0.0075u2009±u2009SD 0.0001) but high haplotype diversity (0.965u2009±u2009SD 0.004). The mtDNA sequences revealed a shallow population genetic structure with a moderate but statistically significant effect of isolation by distance. Demographic history analyses using mtDNA sequences suggested a post‐pleistocene population expansion. Paleodistribution reconstruction projected that the potential habitat of the Assam macaque was confined to the lower elevations of central Nepal during the Last Glacial Maximum. With the onset of the Holocene climatic optimum, the glacial refugia population experienced eastward range expansion to higher elevations. We conclude that the low genetic diversity and shallow population genetic structure of the Assam macaque population in the Nepal Himalaya region are the consequence of recent demographic and spatial expansion.

Patterns and underlying mechanisms of non-volant small mammal richness along two contrasting mountain slopes in southwestern China

The species richness patterns of small mammals and the processes shaping them in two gradients of a mountain with different spatial and climatic characteristics were examined using standard sampling scheme. We trapped 2,006 small mammals representing 37 species, along elevational gradients on both western and eastern slopes of the Ailao Mountains, Southwest China. Using mid-domain effect model, model selection and model averaging, we examined the effects of slope, area, mean annual temperature (MAT), mean annual humidity (MAH), productivity, plant species richness (PSR) and the mid-domain effect (MDE) on the patterns of small mammal diversity. The hump-shaped patterns were favored along the elevational gradient, but shapes of diversity curves were different on the contrasting slopes. Area and productivity were the most important factors in explaining the variation of total species richness. However, for each specific group of small mammals (i.e. insectivores vs. rodents, large-ranged vs. small-ranged species, endemic vs. non-endemic species), the peaks of species richness and their primary drivers varied. The major explanatory factors for richness pattern of each small mammal group were not significantly different between the slopes, suggesting the existence of the general underlying mechanisms on two slopes of a mountain.

Tumor spread through air space (STAS) is an important predictor of clinical outcome in stage IA lung adenocarcinoma

Despite an expanding armamentarium of therapies in recent years, lung cancer remains the leading cause of cancer-related deaths globally (1). Approximately 80% of lung cancers diagnosed worldwide are classified as non-small cell lung cancer (NSCLC), with adenocarcinoma being the most common histologic subtype. Tumor spread through air spaces (STAS) has recently been recognized as an important pattern of tumor invasion in early stage lung adenocarcinoma (2). Indeed, multiple independent groups have determined STAS to have a significant prognostic impact on recurrence in patients with resected stage I lung adenocarcinoma (3-5).

Shifted focus of bronchoalveolar lavage in patients with suspected thoracic malignancy: an analysis of 224 patients

BACKGROUNDnBronchoscopies are extensively adopted for diagnosing and staging thoracic malignancies, but studies are missing as how to keep the process streamlined and more efficient. To evaluate current role of bronchoalveolar lavage (BAL) for cancer and possible infection diagnosis when practicing comprehensive bronchoscopy for patients suspected with thoracic malignancy, and provide foundation for possible practice modification.nnnMETHODSnWe retrospectively analyzed a prospectively kept database of immunocompetent patients undergoing bronchoscopy for suspected non-hematologic malignancies. Clinical, radiographic data, bronchoscopic sampling techniques and diagnostic results were recorded. Initially undiagnostic patients were followed up for 2 years for a definitive diagnosis.nnnRESULTSnOf 224 patients included, 179 (79.9%) were confirmed with active thoracic malignancies. BAL diagnostic yield of cancer based on different radiographic characters of target lesion are as follow: isolated lymphadenopathies 0%, central lesions 45.5%, peripheral masses (diameter ≥3 cm) 21.4%, peripheral large nodules (2≤ diameter <3 cm) 15.8%, and peripheral small nodules (diameter <2 cm) 7.1%, while composite bronchoscopy achieved diagnostic yield of 93.3%, 95.5%, 91.7%, 76.9%, and 66.7% in corresponding lesion types. No cancer was diagnosed solely by BAL-cytology. Proportions of patients with positive BAL culture did not differ significantly between patients with and without pre-test suspicion for infections (P=0.199). In multivariable analysis, infections were associated with age ≥75 (OR 3.0; 95% CI: 1.29-7.06), chronic obstructive pulmonary disease (COPD) (OR 2.7; 95% CI: 1.14-6.26) and diabetes mellitus (DM) (OR 4.5; 95% CI: 1.90-10.44).nnnCONCLUSIONSnOmitting BAL cytology in settings of comprehensive bronchoscopy may not compromise cancer diagnosis. For patients primarily suspected with thoracic malignancy, performing BAL culture only based on clinical suspicion could miss important infectious etiology.

Identifying patterns of care for elderly patients with non-surgically treated stage III non-small cell lung cancer: an analysis of the national cancer database

BackgroundTo compare patterns of care for elderly patients versus non-elderly patients with non-surgically treated stage III non-small cell lung cancer (NSCLC) using the National Cancer Database (NCDB). We hypothesize that elderly patients are less likely to receive curative treatments, including concurrent chemoradiation (CCRT), compared to non-elderly patients.MethodsWe identified patients from the NCDB between 2003 and 2014 with non-surgically treated stage III NSCLC. We defined elderly as ≥70xa0years old and non-elderly <70xa0years old. Treatment categories included: no treatment, palliative treatment (chemotherapy alone, radiation (RT) alone <59.4xa0Gy or chemoradiation (CRT)u2009<59.4xa0Gy), or definitive treatment (RT alonexa0≥59.4xa0Gy or CRTu2009≥59.4xa0Gy). Differences in treatment between elderly and non-elderly were tested using the χ2 test.ResultsWe identified 57,602 elderly and 55,928 non-elderly patients. More elderly patients received no treatment (24.5% vs. 13.2%, Pu2009<xa00.0001) and the elderly were less likely to receive definitive treatment (48.5% vs. 56.3%, Pu2009<xa00.0001). CCRT was delivered in a significantly smaller proportion of elderly vs. non-elderly patients (66.0% vs. 78.9%, Pu2009<xa00.0001 in patients treated with definitive intent; 32.0% vs. 44.5%, Pu2009<xa00.0001 in patients receiving any treatment; and 24.2% vs. 38.6%, Pu2009<xa00.0001 amongst all patients).ConclusionsIn this large study of patients with non-surgically treated stage III NSCLC, elderly patients were less likely to receive any treatment or treatment with definitive intent compared to the non-elderly. The lack of use of concurrent or sequential chemotherapy in the elderly with stage III NSCLC suggests that the optimal treatment approach for this vulnerable population remains undefined.

Rapid and Highly Sensitive Detection of Therapeutically Relevant Oncogenic Driver Mutations in EBUS-TBNA Specimens From Patients With Lung Adenocarcinoma

&NA; We compared light cycler reverse transcription polymerase chain reaction (LCRT‐PCR) and next generation sequencing (NGS) to detect exon 19 deletion of epidermal growth factor receptor (EGFRdelEx19) and Kirsten rat sarcoma 2 viral oncogene homolog (KRAS) exon 2 mutations in endobronchial ultrasound‐guided transbronchial needle aspirations (EBUS‐TBNAs). LCRT‐PCR additionally detected 2 KRAS exon 2 mutations and 3 EGFRdelEx19 mutations that were not detected using NGS. LCRT‐PCR is a highly sensitive method to rapidly detect mutations of therapeutic relevance. Background: First‐line afatinib treatment prolongs overall survival in patients with metastatic non–small‐cell lung cancer (NSCLC) harboring exon 19 deletion of epidermal growth factor receptor (EGFRdelEx19) mutations. In contrast, Kirsten rat sarcoma 2 viral oncogene homolog (KRAS) mutations are negative predictors for benefit from EGFR‐targeting agents. Endobronchial ultrasound‐guided transbronchial needle aspiration (EBUS‐TBNA) is well‐established for lung cancer diagnosis and staging. Next generation sequencing (NGS) allows for simultaneous interrogation for multiple mutations but has limitations (required tumor tissue amount, assay times). Reverse transcription polymerase chain reaction (RT‐PCR) using light‐Cycler technology (LCRT‐PCR) can rapidly and sensitively detect somatic mutations from NSCLC patients. In the present study, we analyzed the feasibility of LCRT‐PCR for rapid EGFRdelEx19 and KRAS exon 2 mutation detection in EBUS‐TBNA samples and compared the LCRT‐PCR and NGS results. Materials and Methods: A total of 48 EBUS‐TBNA samples from 47 patients with a confirmed diagnosis of pulmonary adenocarcinoma were analyzed using LCRT‐PCR (as previously described) and NGS (MiSeq; Illumina) using targeted resequencing and a customized multiplex PCR panel. The processing time was ˜1 week for the NGS and < 24 hours for the LCRT‐PCR analyses. Results: All (100%) EGFRdelEx19 and KRAS exon 2 mutations detected by NGS were detected by LCRT‐PCR. In addition, LCRT‐PCR detected 2 KRAS exon 2 mutations and 3 EGFRdelEx19 mutations that were not detected by NGS. Conclusion: LCRT‐PCR is a highly sensitive method to rapidly detect mutations of therapeutic relevance (eg, EGFRdelEx19 and KRAS exon 2) in EBUS‐TBNAs from NSCLC patients. It is of value as an initial assay for first‐line treatment decisions.

Cancer immune checkpoint blockade therapy and its associated autoimmune cardiotoxicity

The immune checkpoint molecules are emerged in the evolution to protect the host from self-attacks by activated T cells. However, cancer cells, as a strategy to survive and expand, can hijack these molecules and mechanisms to suppress T cell-mediated immune responses. Therefore, an idea of blocking the checkpoint molecules to enhance the anti-tumor activities of the host immune system has been developed and applied to the cancer therapy after discovery of the inhibitory T cell co-receptor, cytotoxic T-lymphocyte associated protein 4 (CTLA-4), and further enhanced on the identification of PD-1 and its ligands. Since 2010, several checkpoint inhibitors have been approved by FDA and many more are in clinical trials. In the treatment of advanced cancers, these inhibitors significantly increased response rates and survival benefits. However, accompanied with the striking results, immune-related adverse events (irAEs) that broadly occurred in many organs were observed and reported, some of which were fatal. Herein, we first review the recent progressions in the research of the immune checkpoint molecules and the application of their blocking antibodies in cancer treatment, and then discuss the cardiac toxicity induced by the therapy and the strategy to monitor, manage this adverse event when it occurs.