Massively parallel base editing to map variant effects in human hematopoiesis.

Systematic evaluation of the impact of genetic variants is critical for the study and treatment of human physiology and disease. While specific mutations can be introduced by genome engineering, we still lack scalable approaches that are applicable to the important setting of primary cells, such as blood and immune cells. Here, we describe the development of massively parallel base-editing screens in human hematopoietic stem and progenitor cells. Such approaches enable functional screens for variant effects across any hematopoietic differentiation state. Moreover, they allow for rich phenotyping through single-cell RNA sequencing readouts and separately for characterization of editing outcomes through pooled single-cell genotyping. We efficiently design improved leukemia immunotherapy approaches, comprehensively identify non-coding variants modulating fetal hemoglobin expression, define mechanisms regulating hematopoietic differentiation, and probe the pathogenicity of uncharacterized disease-associated variants. These strategies will advance effective and high-throughput variant-to-function mapping in human hematopoiesis to identify the causes of diverse diseases.

Mapping transcriptomic vector fields of single cells.

Single-cell (sc)RNA-seq, together with RNA velocity and metabolic labeling, reveals cellular states and transitions at unprecedented resolution. Fully exploiting these data, however, requires kinetic models capable of unveiling governing regulatory functions. Here, we introduce an analytical framework dynamo (https://github.com/aristoteleo/dynamo-release), which infers absolute RNA velocity, reconstructs continuous vector fields that predict cell fates, employs differential geometry to extract underlying regulations, and ultimately predicts optimal reprogramming paths and perturbation outcomes. We highlight dynamo's power to overcome fundamental limitations of conventional splicing-based RNA velocity analyses to enable accurate velocity estimations on a metabolically labeled human hematopoiesis scRNA-seq dataset. Furthermore, differential geometry analyses reveal mechanisms driving early megakaryocyte appearance and elucidate asymmetrical regulation within the PU.1-GATA1 circuit. Leveraging the least-action-path method, dynamo accurately predicts drivers of numerous hematopoietic transitions. Finally, in silico perturbations predict cell-fate diversions induced by gene perturbations. Dynamo, thus, represents an important step in advancing quantitative and predictive theories of cell-state transitions.

Deciphering cell states and genealogies of human haematopoiesis.

The human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived haematopoietic stem cells (HSCs)1. Perturbations to this process underlie diverse diseases, but the clonal contributions to human haematopoiesis and how this changes with age remain incompletely understood. Although recent insights have emerged from barcoding studies in model systems2-5, simultaneous detection of cell states and phylogenies from natural barcodes in humans remains challenging. Here we introduce an improved, single-cell lineage-tracing system based on deep detection of naturally occurring mitochondrial DNA mutations with simultaneous readout of transcriptional states and chromatin accessibility. We use this system to define the clonal architecture of HSCs and map the physiological state and output of clones. We uncover functional heterogeneity in HSC clones, which is stable over months and manifests as both differences in total HSC output and biases towards the production of different mature cell types. We also find that the diversity of HSC clones decreases markedly with age, leading to an oligoclonal structure with multiple distinct clonal expansions. Our study thus provides a clonally resolved and cell-state-aware atlas of human haematopoiesis at single-cell resolution, showing an unappreciated functional diversity of human HSC clones and, more broadly, paving the way for refined studies of clonal dynamics across a range of tissues in human health and disease.

HBO1 is required for the maintenance of leukaemia stem cells.

Acute myeloid leukaemia (AML) is a heterogeneous disease characterized by transcriptional dysregulation that results in a block in differentiation and increased malignant self-renewal. Various epigenetic therapies aimed at reversing these hallmarks of AML have progressed into clinical trials, but most show only modest efficacy owing to an inability to effectively eradicate leukaemia stem cells (LSCs)1. Here, to specifically identify novel dependencies in LSCs, we screened a bespoke library of small hairpin RNAs that target chromatin regulators in a unique ex vivo mouse model of LSCs. We identify the MYST acetyltransferase HBO1 (also known as KAT7 or MYST2) and several known members of the HBO1 protein complex as critical regulators of LSC maintenance. Using CRISPR domain screening and quantitative mass spectrometry, we identified the histone acetyltransferase domain of HBO1 as being essential in the acetylation of histone H3 at K14. H3 acetylated at K14 (H3K14ac) facilitates the processivity of RNA polymerase II to maintain the high expression of key genes (including Hoxa9 and Hoxa10) that help to sustain the functional properties of LSCs. To leverage this dependency therapeutically, we developed a highly potent small-molecule inhibitor of HBO1 and demonstrate its mode of activity as a competitive analogue of acetyl-CoA. Inhibition of HBO1 phenocopied our genetic data and showed efficacy in a broad range of human cell lines and primary AML cells from patients. These biological, structural and chemical insights into a therapeutic target in AML will enable the clinical translation of these findings.

Inferring gene regulation from stochastic transcriptional variation across single cells at steady state.

Regulatory relationships between transcription factors (TFs) and their target genes lie at the heart of cellular identity and function; however, uncovering these relationships is often labor-intensive and requires perturbations. Here, we propose a principled framework to systematically infer gene regulation for all TFs simultaneously in cells at steady state by leveraging the intrinsic variation in the transcriptional abundance across single cells. Through modeling and simulations, we characterize how transcriptional bursts of a TF gene are propagated to its target genes, including the expected ranges of time delay and magnitude of maximum covariation. We distinguish these temporal trends from the time-invariant covariation arising from cell states, and we delineate the experimental and technical requirements for leveraging these small but meaningful cofluctuations in the presence of measurement noise. While current technology does not yet allow adequate power for definitively detecting regulatory relationships for all TFs simultaneously in cells at steady state, we investigate a small-scale dataset to inform future experimental design. This study supports the potential value of mapping regulatory connections through stochastic variation, and it motivates further technological development to achieve its full potential.

Clinical study of camrelizumab combined with docetaxel and carboplatin as a neoadjuvant treatment for locally advanced oesophageal squamous cell carcinoma.

Herein, we aimed to evaluate the efficacy and safety of camrelizumab combined with docetaxel and carboplatin as a neoadjuvant treatment for locally advanced oesophageal squamous cell carcinoma (OSCC). Fifty-one patients with OSCC, treated from July 2020 to October 2022, were analyzed. Of them, 41 patients underwent surgery 4-8 weeks after undergoing two cycles of camrelizumab (200 mg IV Q3W) combined with docetaxel (75 mg/m2 IV Q3W) and carboplatin (area under the curve = 5-6 IV Q3W). The primary endpoint was the pathological complete response rate. All 51 patients (100%) experienced treatment-related grades 1-2 adverse events, and 2 patients (3.9%) experienced grade 4 events (including elevated alanine transaminase/aspartate transferase levels and Guillain-Barre syndrome). Fifty patients were evaluated for the treatment efficacy. Of them, 13 achieved complete response, and the objective response rate was 74%. Only 41 patients underwent surgical treatment. The pathological complete response rate was 17.1%, the major pathological response rate was 63.4%, and the R0 resection rate was 100%. Approximately 22% of the patients had tumor regression grades 0. Eight patients (19.5%) developed surgery-related complications. The median follow-up time was 18 months (range: 3-29 months). Four patients experienced disease progression, while four died. The median disease-free survival and overall survival were not reached. Camrelizumab combined with docetaxel and carboplatin is an effective and safe neoadjuvant treatment for locally advanced OSCC. This regimen may afford a potential strategy to treat patients with locally advanced OSCC.

Environmental damage compensation for illegal solid waste dumping in China.

China aims to improve its system for pursuing environmental damage compensation environmental violation cases. To hold violators accountable, China has an effective system for the identification and assessment (I&A) of environmental damage. This study selected a typical case of the illegal dumping of solid waste (IDSW) in China to analyze the causes, the degree, and characteristics of environmental damage, focusing on components such as the physical quantification and valuation of damage. The findings were as follows: (1) Compensation claimants and obligors consider baseline damage confirmation and causality analysis key components of I&A. (2) The I&A process for a specific case needs to focus on key nodes such as the type, location, and duration of IDSW. (3) Restraining IDSW requires accurately quantifying the physical and value-related losses caused by solid waste dumping. (4) In the selected case study, the damage from environmental contamination caused by the IDSW incident amounted to 3938,990 yuan, including an environmental damage value of 3651,990 yuan and a transaction cost of 287,000 yuan. Both parties accepted the I&A calculation process in this case, and the desired punishment effect was achieved. Hence, the case study demonstrated that accurate I&A is the technical basis for environmental damage compensation. Thus, in the future, more attention should be paid to the role of scientific and technological means and knowledge reserves in the I&A of environmental damage.

The transcription factor Nerfin-1 prevents reversion of neurons into neural stem cells.

Cellular dedifferentiation is the regression of a cell from a specialized state to a more multipotent state and is implicated in cancer. However, the transcriptional network that prevents differentiated cells from reacquiring stem cell fate is so far unclear. Neuroblasts (NBs), the Drosophila neural stem cells, are a model for the regulation of stem cell self-renewal and differentiation. Here we show that the Drosophila zinc finger transcription factor Nervous fingers 1 (Nerfin-1) locks neurons into differentiation, preventing their reversion into NBs. Following Prospero-dependent neuronal specification in the ganglion mother cell (GMC), a Nerfin-1-specific transcriptional program maintains differentiation in the post-mitotic neurons. The loss of Nerfin-1 causes reversion to multipotency and results in tumors in several neural lineages. Both the onset and rate of neuronal dedifferentiation in nerfin-1 mutant lineages are dependent on Myc- and target of rapamycin (Tor)-mediated cellular growth. In addition, Nerfin-1 is required for NB differentiation at the end of neurogenesis. RNA sequencing (RNA-seq) and chromatin immunoprecipitation (ChIP) analysis show that Nerfin-1 administers its function by repression of self-renewing-specific and activation of differentiation-specific genes. Our findings support the model of bidirectional interconvertibility between neural stem cells and their post-mitotic progeny and highlight the importance of the Nerfin-1-regulated transcriptional program in neuronal maintenance.

TWO-SIGMA: A novel two-component single cell model-based association method for single-cell RNA-seq data.

In this paper, we develop TWO-SIGMA, a TWO-component SInGle cell Model-based Association method for differential expression (DE) analyses in single-cell RNA-seq (scRNA-seq) data. The first component models the probability of "drop-out" with a mixed-effects logistic regression model and the second component models the (conditional) mean expression with a mixed-effects negative binomial regression model. TWO-SIGMA is extremely flexible in that it: (i) does not require a log-transformation of the outcome, (ii) allows for overdispersed and zero-inflated counts, (iii) accommodates a correlation structure between cells from the same individual via random effect terms, (iv) can analyze unbalanced designs (in which the number of cells does not need to be identical for all samples), (v) can control for additional sample-level and cell-level covariates including batch effects, (vi) provides interpretable effect size estimates, and (vii) enables general tests of DE beyond two-group comparisons. To our knowledge, TWO-SIGMA is the only method for analyzing scRNA-seq data that can simultaneously accomplish each of these features. Simulations studies show that TWO-SIGMA outperforms alternative regression-based approaches in both type-I error control and power enhancement when the data contains even moderate within-sample correlation. A real data analysis using pancreas islet single-cells exhibits the flexibility of TWO-SIGMA and demonstrates that incorrectly failing to include random effect terms can have dramatic impacts on scientific conclusions. TWO-SIGMA is implemented in the R package twosigma available at https://github.com/edvanburen/twosigma.

Simple security proof of coherent-one-way quantum key distribution.

Coherent-one-way quantum key distribution (COW-QKD), which requires a simple experimental setup and has the ability to withstand photon-number-splitting attacks, has been not only experimentally implemented but also commercially applied. However, recent studies have shown that the current COW-QKD system is insecure and can only distribute secret keys safely within 20 km of the optical fiber length. In this study, we propose a practical implementation of COW-QKD by adding a two-pulse vacuum state as a new decoy sequence. This proposal maintains the original experimental setup as well as the simplicity of its implementation. Utilizing detailed observations on the monitoring line to provide an analytical upper bound on the phase error rate, we provide a high-performance COW-QKD asymptotically secure against coherent attacks. This ensures the availability of COW-QKD within 100 km and establishes theoretical foundations for further applications.

A full-face mask for protection against respiratory infections.

BACKGROUND: Aerosols and droplets are the transmission routes of many respiratory infectious diseases. The COVID-19 management guidance recommends against the use of nebulized inhalation therapy directly in the emergency room or in an ambulance to prevent possible viral transmission. The three-dimensional printing method was used to develop an aerosol inhalation treatment mask that can potentially prevent aerosol dispersion. We conducted this utility validation study to understand the practicability of this new nebulizer mask system. RESULTS: The fit test confirmed that the filter can efficiently remove small particles. The different locations of the mask had an excellent fit with a high pressure making a proper face seal usability. The full-face mask appeared to optimize filtration with pressure and is an example of materials that perform well for improvised respiratory protection using this design. The filtering effect test confirmed that the contamination of designated locations could be protected when using the mask with filters. As in the clinical safety test, a total of 18 participants (10 [55.6%] females; aged 33.1 ± 0.6 years) were included in the final analysis. There were no significant changes in SPO2, EtCO2, HR, SBP, DBP, and RR at the beginning, 20th, 40th, or 60th minutes of the test (all p >.05). The discomfort of wearing a mask increased slightly after time but remained within the tolerable range. The vision clarity score did not significantly change during the test. The mask also passed the breathability test. CONCLUSION: The results of our study showed that this mask performed adequately in the fit test, the filtering test, and the clinical safety test. The application of a full-face mask with antiviral properties, together with the newly designed shape of a respirator that respects the natural curves of a human face, will facilitate the production of personal protective equipment with a highly efficient filtration system. METHODS: We conducted three independent tests in this validation study: (1) a fit test to calculate the particle number concentration and its association with potential leakage; (2) a filtering effect test to verify the mask's ability to contain aerosol spread; and (3) a clinical safety test to examine the clinical safety, comfortableness, and visual clarity of the mask.

Aryl hydrocarbon receptor activation-mediated vascular toxicity of ambient fine particulate matter: contribution of polycyclic aromatic hydrocarbons and osteopontin as a biomarker.

BACKGROUND: Exposure to ambient fine particulate matter (PM2.5) is associated with vascular diseases. Polycyclic aromatic hydrocarbons (PAHs) in PM2.5 are highly hazardous; however, the contribution of PM2.5-bound PAHs to PM2.5-associated vascular diseases remains unclear. The ToxCast high-throughput in vitro screening database indicates that some PM2.5-bound PAHs activate the aryl hydrocarbon receptor (AhR). The present study investigated whether the AhR pathway is involved in the mechanism of PM2.5-induced vascular toxicity, identified the PAH in PM2.5 that was the major contributor of AhR activation, and identified a biomarker for vascular toxicity of PM2.5-bound PAHs. RESULTS: Treatment of vascular smooth muscle cells (VMSCs) with an AhR antagonist inhibited the PM2.5-induced increase in the cell migration ability; NF-κB activity; and expression of cytochrome P450 1A1 (CYP1A1), 1B1 (CYP1B1), interleukin-6 (IL-6), and osteopontin (OPN). Most PM2.5-bound PAHs were extracted into the organic fraction, which drastically enhanced VSMC migration and increased mRNA levels of CYP1A1, CYP1B1, IL-6, and OPN. However, the inorganic fraction of PM2.5 moderately enhanced VSMC migration and only increased IL-6 mRNA levels. PM2.5 increased IL-6 secretion through NF-κB activation; however, PM2.5 and its organic extract increased OPN secretion in a CYP1B1-dependent manner. Inhibiting CYP1B1 activity and silencing OPN expression prevented the increase in VSMC migration ability caused by PM2.5 and its organic extract. The AhR activation potencies of seven PM2.5-bound PAHs, reported in the ToxCast database, were strongly correlated with their capabilities of enhancing the migration ability of VSMCs. Benzo(k)fluoranthene (BkF) contributed the most to the AhR agonistic activity of ambient PM2.5-bound PAHs. The association between PM2.5-induced vascular toxicity, AhR activity, and OPN secretion was further verified in mice; PM2.5-induced intimal hyperplasia in pulmonary small arteries and OPN secretion were alleviated in mice with low AhR affinity. Finally, urinary concentrations of 1-hydroxypyrene, a major PAH metabolite, were positively correlated with plasma OPN levels in healthy humans. CONCLUSIONS: The present study offers in vitro, animal, and human evidences supporting the importance of AhR activation for PM2.5-induced vascular toxicities and that BkF was the major contributor of AhR activation. OPN is an AhR-dependent biomarker of PM2.5-induced vascular toxicity. The AhR activation potency may be applied in the risk assessment of vascular toxicity in PAH mixtures.

Paper-Based Microfluidics Perform Mixing Effects by Utilizing Planar Constricted-Expanded Structures to Enhance Chaotic Advection.

This study aimed to design and fabricate planar constricted-expanded structures that are integrated into paper-based channels in order to enhance their chaotic advection and improve their mixing performance. Chromatography papers were used to print paper-based microfluidics using a solid-wax printer. Three different constricted-expanded structures-i.e., zigzag, crossed, and curved channels-were designed in order to evaluate their mixing performance in comparison with that of straight channels. A numerical simulation was performed in order to investigate the mixing mechanism, and to examine the ways in which the planar constricted-expanded structures affected the flow patterns. The experimental and numerical results indicated that the proposed structures can successfully mix confluents. The experimental results revealed that the mixing indices (σ) rose from the initial 20.1% (unmixed) to 34.5%, 84.3%, 87.3%, and 92.4% for the straight, zigzag, curved, and cross-shaped channels, respectively. In addition, the numerical calculations showed a reasonable agreement with the experimental results, with a variation in the range of 1.0-11.0%. In future, we hope that the proposed passive paper-based mixers will be a crucial component in the application of paper-based microfluidic devices.

Nanoporous Metal Phosphonate Hybrid Materials as a Novel Platform for Emerging Applications: A Critical Review.

Nanoporous metal phosphonates are propelling the rapid development of emerging energy storage, catalysis, environmental intervention, and biology, the performances of which touch many fundamental aspects of portable electronics, convenient transportation, and sustainable energy conversion systems. Recent years have witnessed tremendous research breakthroughs in these fields in terms of the fascinating pore properties, the structural periodicity, and versatile skeletons of porous metal phosphonates. This review presents recent milestones of porous metal phosphonate research, from the diversified synthesis strategies for controllable pore structures, to several important applications including adsorption and separation, energy conversion and storage, heterogeneous catalysis, membrane engineering, and biomaterials. Highlights of porous structure design for metal phosphonates are described throughout the review and the current challenges and perspectives for future research in this field are discussed at the end. The aim is to provide some guidance for the rational preparation of porous metal phosphonate materials and promote further applications to meet the urgent demands in emerging applications.

Efficient quantum digital signatures without symmetrization step.

Quantum digital signatures (QDS) exploit quantum laws to guarantee non-repudiation, unforgeability and transferability of messages with information-theoretic security. Current QDS protocols face two major restrictions, including the requirement of the symmetrization step with additional secure classical channels and the quadratic scaling of the signature rate with the probability of detection events. Here, we present an efficient QDS protocol to overcome these issues by utilizing the classical post-processing operation called post-matching method. Our protocol does not need the symmetrization step, and the signature rate scales linearly with the probability of detection events. Simulation results show that the signature rate is three orders of magnitude higher than the original protocol in a 100-km-long fiber. This protocol is compatible with existing quantum communication infrastructure, therefore we anticipate that it will play a significant role in providing digital signatures with unconditional security.

Secure and practical multiparty quantum digital signatures.

Quantum digital signatures (QDSs) promise information-theoretic security against repudiation and forgery of messages. Compared with currently existing three-party QDS protocols, multiparty protocols have unique advantages in the practical case of more than two receivers when sending a mass message. However, complex security analysis, numerous quantum channels and low data utilization efficiency make it intractable to expand three-party to multiparty scenario. Here, based on six-state non-orthogonal encoding protocol, we propose an effective multiparty QDS framework to overcome these difficulties. The number of quantum channels in our protocol only linearly depends on the number of users. The post-matching method is introduced to enhance data utilization efficiency and make it linearly scale with the probability of detection events even for five-party scenario. Our work compensates for the absence of practical multiparty protocols, which paves the way for future QDS networks.

Long-distance twin-field quantum key distribution with entangled sources.

Twin-field quantum key distribution (TFQKD), using single-photon-type interference, offers a way to exceed the rate-distance limit without quantum repeaters. However, it still suffers from photon losses and dark counts, which impose an ultimate limit on its transmission distance. In this Letter, we propose a scheme to implement TFQKD with an entangled coherent state source in the middle to increase its range, as well as comparing its performance under coherent attacks with that of TFQKD variants. Simulations show that our protocol has a theoretical distance advantage of 400 km. Moreover, the scheme has great robustness against the misalignment error and finite-size effects. Our work is a promising step toward long-distance secure communication and is greatly compatible with future global quantum networks.

Clinical implications of prospective genomic profiling of metastatic breast cancer patients.

BACKGROUND: Metastatic breast cancer remains incurable. Next-generation sequencing (NGS) offers the ability to identify actionable genomic alterations in tumours which may then be matched with targeted therapies, but the implementation and utility of this approach is not well defined for patients with metastatic breast cancer. METHODS: We recruited patients with advanced breast cancer of any subtype for prospective targeted NGS of their most recent tumour samples, using a panel of 108 breast cancer-specific genes. Genes were classified as actionable or non-actionable using the European Society of Medical Oncology Scale for Clinical Actionability of Molecular Targets (ESCAT) guidelines. RESULTS: Between February 2014 and May 2019, 322 patients were enrolled onto the study, with 72% (n = 234) of patients successfully sequenced (n = 357 samples). The majority (74%, n = 171) of sequenced patients were found to carry a potentially actionable alteration, the most common being a PIK3CA mutation. Forty-three percent (n = 74) of patients with actionable alterations were referred for a clinical trial or referred for confirmatory germline testing or had a change in therapy outside of clinical trials. We found alterations in AKT1, BRCA2, CHEK2, ESR1, FGFR1, KMT2C, NCOR1, PIK3CA and TSC2 to be significantly enriched in our metastatic population compared with primary breast cancers. Concordance between primary and metastatic samples for key driver genes (TP53, ERBB2 amplification) was > 75%. Additionally, we found that patients with a higher number of mutations had a significantly worse overall survival. CONCLUSION: Genomic profiling of patients with metastatic breast cancer can have clinical implications and should be considered in all suitable patients.

Circulating tumour DNA in metastatic breast cancer to guide clinical trial enrolment and precision oncology: A cohort study.

BACKGROUND: Metastatic breast cancer (mBC) is a heterogenous disease with increasing availability of targeted therapies as well as emerging genomic markers of therapeutic resistance, necessitating timely and accurate molecular characterization of disease. As a minimally invasive test, analysis of circulating tumour DNA (ctDNA) is well positioned for real-time genomic profiling to guide treatment decisions. Here, we report the results of a prospective testing program established to assess the feasibility of ctDNA analysis to guide clinical management of mBC patients. METHODS AND FINDINGS: Two hundred thirty-four mBC patients (median age 54 years) were enrolled between June 2015 and October 2018 at the Peter MacCallum Cancer Centre, Melbourne, Australia. Median follow-up was 15 months (range 1-46). All patient samples at the time of enrolment were analysed in real time for the presence of somatic mutations. Longitudinal plasma testing during the course of patient management was also undertaken in a subset of patients (n = 67, 28.6%), according to clinician preference, for repeated molecular profiling or disease monitoring. Detection of somatic mutations from patient plasma was performed using a multiplexed droplet digital PCR (ddPCR) approach to identify hotspot mutations in PIK3CA, ESR1, ERBB2, and AKT1. In parallel, subsets of samples were also analysed via next-generation sequencing (targeted panel sequencing and low-coverage whole-genome sequencing [LC-WGS]). The sensitivity of ddPCR and targeted panel sequencing to identify actionable mutations was compared. Results were discussed at a multidisciplinary breast cancer meeting prior to treatment decisions. ddPCR and targeted panel sequencing identified at least 1 actionable mutation at baseline in 80/234 (34.2%) and 62/159 (39.0%) of patients tested, respectively. Combined, both methods detected an actionable alteration in 104/234 patients (44.4%) through baseline or serial ctDNA testing. LC-WGS was performed on 27 patients from the cohort, uncovering several recurrently amplified regions including 11q13.3 encompassing CCND1. Increasing ctDNA levels were associated with inferior overall survival, whether assessed by ddPCR, targeted sequencing, or LC-WGS. Overall, the ctDNA results changed clinical management in 40 patients including the direct recruitment of 20 patients to clinical trials. Limitations of the study were that it was conducted at a single site and that 31.3% of participants were lost to follow-up. CONCLUSION: In this study, we found prospective ctDNA testing to be a practical and feasible approach that can guide clinical trial enrolment and patient management in mBC.

Hybrid III-V-on-SOI optical spot size converter by self-aligned selective undercut dry etching of Si.

A technology called self-aligned selective undercut dry etching processing has been demonstrated for fabricating a highly efficient hybrid optical spot size converter (SSC) on a Si-on-insulator (SOI) template. The process was based on a bonded wafer between the upper InP-based multiple quantum well heterostructure and the lower SOI substrate. After defining the mask on the upper InP-based ridge waveguide, CF4/O2 dry reactive ion etching was then used for selective undercut etching of the Si material from the surrounding materials, forming a vertical waveguide coupler of the optical SSC. The lower waveguide, whose dimension is even smaller than the upper one, can thus be vertically self-aligned to the top ridge via an independent processing step. A laterally tapered waveguide ranging from 0.3 to 3 µm in width on the upper InP waveguide was fabricated. The phase-matching condition of the vertical coupler leads to a length of 45 µm and extracts 88% conversion efficiency. The selective undercut etching processing in III-V/SOI material provides a vertical self-alignment scheme for realizing compact and submicron scale heterogeneous integration in a Si photonics template.